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Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.jmoldx.2011.01.006openalex-snapshot
Hybrid Capture and Next-Generation Sequencing Identify Viral Integration Sites from Formalin-Fixed, Paraffin-Embedded Tissue
inferredcites →https://doi.org/10.1016/j.mib.2008.09.011openalex-snapshot
A renaissance for the pioneering 16S rRNA gene
inferredcites →https://doi.org/10.1016/j.ympev.2010.03.026openalex-snapshot
Placement of Conopidae (Diptera) within Schizophora based on mtDNA and nrDNA gene regions
inferredcites →https://doi.org/10.1038/nmeth.1343openalex-snapshot
Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection
inferredcites →https://doi.org/10.1038/srep00074openalex-snapshot
Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA
inferredcites →https://doi.org/10.1038/srep09687openalex-snapshot
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform
inferredcites →https://doi.org/10.1038/srep15894openalex-snapshot
A DNA Mini-Barcoding System for Authentication of Processed Fish Products
inferredcites →https://doi.org/10.1073/pnas.0905845106openalex-snapshot
A DNA barcode for land plants
inferredcites →https://doi.org/10.1073/pnas.1117018109openalex-snapshot
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
inferredcites →https://doi.org/10.1073/pnas.1209160109openalex-snapshot
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna
inferredcites →https://doi.org/10.1073/pnas.1406468111openalex-snapshot
Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics
inferredcites →https://doi.org/10.1073/pnas.1424997112openalex-snapshot
DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity
inferredcites →https://doi.org/10.1073/pnas.74.12.5463openalex-snapshot
DNA sequencing with chain-terminating inhibitors
inferredcites →https://doi.org/10.1089/10665270050081478openalex-snapshot
A Greedy Algorithm for Aligning DNA Sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/btr026openalex-snapshot
Quality control and preprocessing of metagenomic datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btr381openalex-snapshot
UCHIME improves sensitivity and speed of chimera detection
inferredcites →https://doi.org/10.1098/rspb.2002.2218openalex-snapshot
Biological identifications through DNA barcodes
inferredcites →https://doi.org/10.1101/gr.120196.111openalex-snapshot
Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens
inferredcites →https://doi.org/10.1111/1755-0998.12236openalex-snapshot
Next‐generation DNA barcoding: using next‐generation sequencing to enhance and accelerate DNA barcode capture from single specimens
inferredcites →https://doi.org/10.1111/1755-0998.12249openalex-snapshot
Sequence capture using PCR ‐generated probes: a cost‐effective method of targeted high‐throughput sequencing for nonmodel organisms
inferredcites →https://doi.org/10.1111/1755-0998.12254openalex-snapshot
Performance comparison of genetic markers for high‐throughput sequencing‐based biodiversity assessment in complex communities
inferredcites →https://doi.org/10.1111/1755-0998.12355openalex-snapshot
Universal and blocking primer mismatches limit the use of high‐throughput DNA sequencing for the quantitative metabarcoding of arthropods
inferredcites →https://doi.org/10.1111/1755-0998.12472openalex-snapshot
Mitochondrial capture enriches mito‐DNA 100 fold, enabling PCR‐free mitogenomics biodiversity analysis
inferredcites →https://doi.org/10.1111/cla.12115openalex-snapshot
$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen‐rich samples
inferredcites →https://doi.org/10.1111/j.1365-294x.2009.04473.xopenalex-snapshot
Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05538.xopenalex-snapshot
Next‐generation sequencing technologies for environmental DNA research
inferredcites →https://doi.org/10.1111/j.1469-8137.2011.03838.xopenalex-snapshot
Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?
inferredcites →https://doi.org/10.1111/j.1471-8286.2007.01678.xopenalex-snapshot
bold : The Barcode of Life Data System (http://www.barcodinglife.org)
inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02920.xopenalex-snapshot
Taxon‐specific PCR for DNA barcoding arthropod prey in bat faeces
inferredcites →https://doi.org/10.1111/jzs.12095openalex-snapshot
Ghost mtDNA haplotypes generated by fortuitous NUMTs can deeply disturb infra-specific genetic diversity and phylogeographic pattern
inferredcites →https://doi.org/10.1111/mec.12480openalex-snapshot
High‐throughput amplicon sequencing of r RNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure
inferredcites →https://doi.org/10.1128/aem.62.2.625-630.1996openalex-snapshot
Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
inferredcites →https://doi.org/10.1128/aem.64.10.3724-3730.1998openalex-snapshot
Bias in Template-to-Product Ratios in Multitemplate PCR
inferredcites →https://doi.org/10.1186/1471-2164-9-214openalex-snapshot
A universal DNA mini-barcode for biodiversity analysis
inferredcites →https://doi.org/10.1186/1472-6785-12-28openalex-snapshot
Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol
inferredcites →https://doi.org/10.1186/1741-7007-5-24openalex-snapshot
Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring
inferredcites →https://doi.org/10.1186/2047-217x-2-4openalex-snapshot
Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
inferredcites →https://doi.org/10.1353/psc.2003.0021openalex-snapshot
Regressions of Length and Width to Predict Arthropod Biomass in the Hawaiian Islands
inferredcites →https://doi.org/10.1371/journal.pone.0013102openalex-snapshot
Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
inferredcites →https://doi.org/10.1371/journal.pone.0014004openalex-snapshot
Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products
inferredcites →https://doi.org/10.1371/journal.pone.0017497openalex-snapshot
Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos
inferredcites →https://doi.org/10.1371/journal.pone.0029973openalex-snapshot
Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities
inferredcites →https://doi.org/10.1371/journal.pone.0056739openalex-snapshot
Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera
inferredcites →https://doi.org/10.1371/journal.pone.0095633openalex-snapshot
Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
inferredcites →https://doi.org/10.1371/journal.pone.0109101openalex-snapshot
Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)
inferredcites →https://doi.org/10.5281/zenodo.15145663openalex-snapshot
Table 1 in A new Gammarus species from Xinjiang Uygur Autonomous Region (China) with a key to Xinjiang freshwater gammarids (Crustacea, Amphipoda, Gammaridae)
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/ece3.5984openalex-snapshot
Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era
inferred← citeshttps://doi.org/10.1002/ecs2.70439openalex-snapshot
Invasive giant river prawns as opportunistic, generalist predators in the Amazon Delta: Insights from metabarcoding
inferred← citeshttps://doi.org/10.1007/s00427-020-00652-xopenalex-snapshot
High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities
inferred← citeshttps://doi.org/10.1016/bs.aecr.2018.01.001openalex-snapshot
Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action
inferred← citeshttps://doi.org/10.1016/bs.aecr.2020.01.001openalex-snapshot
Advances and prospects of environmental DNA in neotropical rainforests
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2020.142622openalex-snapshot
Methodology of fish eDNA and its applications in ecology and environment
inferred← citeshttps://doi.org/10.1017/qua.2022.46openalex-snapshot
Ancient DNA from speleothems: opportunity or challenge?
inferred← citeshttps://doi.org/10.1038/s41598-017-13157-xopenalex-snapshot
DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient
inferred← citeshttps://doi.org/10.1038/s41598-017-17333-xopenalex-snapshot
Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding
inferred← citeshttps://doi.org/10.1038/s41598-018-22505-4openalex-snapshot
Automated high throughput animal CO1 metabarcode classification
inferred← citeshttps://doi.org/10.1093/gigascience/giac020openalex-snapshot
Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0001openalex-snapshot
Introduction to environmental DNA (eDNA)
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0002openalex-snapshot
DNA metabarcode choice and design
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0003openalex-snapshot
Reference databases
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0006openalex-snapshot
DNA amplification and multiplexing
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0008openalex-snapshot
DNA metabarcoding data analysis
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0009openalex-snapshot
Single-species detection
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0010openalex-snapshot
Environmental DNA for functional diversity
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0011openalex-snapshot
Some early landmark studies
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0012openalex-snapshot
Freshwater ecosystems
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0013openalex-snapshot
Marine environments
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0014openalex-snapshot
Terrestrial ecosystems
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0016openalex-snapshot
Host-associated microbiota
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0018openalex-snapshot
Analysis of bulk samples
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.003.0019openalex-snapshot
The future of eDNA metabarcoding
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.005.0001openalex-snapshot
Examples of primer pairs available for DNA metabarcoding
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.005.0002openalex-snapshot
Three-hundred and eighty-four (384) tags of eight nucleotides, with at least three differences among them
inferred← citeshttps://doi.org/10.1093/oso/9780198767220.005.0003openalex-snapshot
Checklist when designing a PCR-based DNA metabarcoding experiment
inferred← citeshttps://doi.org/10.1111/1755-0998.12928openalex-snapshot
Capture enrichment of aquatic environmental DNA: A first proof of concept
inferred← citeshttps://doi.org/10.1111/1755-0998.13069openalex-snapshot
Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes
inferred← citeshttps://doi.org/10.1111/1755-0998.13088openalex-snapshot
Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol
inferred← citeshttps://doi.org/10.1111/1755-0998.13201openalex-snapshot
Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes
inferred← citeshttps://doi.org/10.1111/1755-0998.13500openalex-snapshot
Capture by hybridization for full‐length barcode‐based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems
inferred← citeshttps://doi.org/10.1111/geb.13156openalex-snapshot
Methods and approaches to advance soil macroecology
inferred← citeshttps://doi.org/10.1111/mec.14478openalex-snapshot
Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis
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The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota
inferred← citeshttps://doi.org/10.1371/journal.pone.0202976openalex-snapshot
Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms
inferred← citeshttps://doi.org/10.1371/journal.pone.0219218openalex-snapshot
An optimised eDNA protocol for detecting fish in lentic and lotic freshwaters using a small water volume
inferred← citeshttps://doi.org/10.1590/1676-0611-bn-2021-1214openalex-snapshot
Metabarcoding advances for ecology and biogeography of Neotropical protists: what do we know, where do we go?
inferred← citeshttps://doi.org/10.23889/suthesis.52895openalex-snapshot
Spatial and seasonal distribution patterns of native and introduced aquatic species based on environmental DNA
inferred← citeshttps://doi.org/10.3389/fevo.2017.00158openalex-snapshot
Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders
inferred← citeshttps://doi.org/10.3389/fevo.2020.00248openalex-snapshot
Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis
inferred← citeshttps://doi.org/10.3389/fevo.2021.735744openalex-snapshot
A Multi-Gene Region Targeted Capture Approach to Detect Plant DNA in Environmental Samples: A Case Study From Coastal Environments
inferred← citeshttps://doi.org/10.3390/insects11030183openalex-snapshot
The Chironomidae (Diptera) of Svalbard and Jan Mayen
inferred← citeshttps://doi.org/10.3897/bdj.5.e10792openalex-snapshot
Arthropod and oligochaete assemblages from grasslands of the southern Kenai Peninsula, Alaska
inferred← citeshttps://doi.org/10.70675/1aecfc48zabb1z4d30za665z5c7e02e5ae99openalex-snapshot
Dynamique des métacommunautés dans les têtes de bassin versant fragmentées : une perspective moléculaire
inferred← citeshttps://doi.org/10.70675/c6e0cd3az6ba5z4847za247z9b74caf1a82aopenalex-snapshot
From functional genes to ecosystem functioning : towards a new integrative vision of biodiversity-function links in hydrosystems
inferred← citeshttps://doi.org/10.7717/peerj.6727openalex-snapshot
Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies
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